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diff --git a/rdf-documentation/dump-probeset.md b/rdf-documentation/dump-probeset.md new file mode 100644 index 0000000..d5729cf --- /dev/null +++ b/rdf-documentation/dump-probeset.md @@ -0,0 +1,95 @@ +# ProbeSet Metadata +## 'dump-probeset' + +## Generated Triples: + +The following SQL query was executed: + +```sql +SELECT IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name)) AS ProbeSetIdName, ProbeSet.Id, ProbeSet.Name, ProbeSet.alias, IFNULL(GeneChip.Name, '') AS GeneChipName, NULLIF(TRIM(ProbeSet.TargetId), '') AS TargetId, ProbeSet.Symbol, ProbeSet.description, NULLIF(TRIM(ProbeSet.Probe_set_target_region), '') AS Probe_set_target_region, ProbeSet.Chr, IFNULL(ProbeSet.Mb, '') AS Mb, IFNULL(ProbeSet.Mb_mm8, '') AS Mb_mm8, IFNULL(ProbeSet.Mb_2016, '') AS Mb_2016, IFNULL(ProbeSet.Probe_set_specificity, '') AS Probe_set_specificity, IFNULL(ProbeSet.Probe_set_BLAT_score, '') AS Probe_set_BLAT_score, IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '') AS Probe_set_Blat_Mb_start, IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '') AS Probe_set_Blat_Mb_start_2016, IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '') AS Probe_set_Blat_Mb_end, IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '') AS Probe_set_Blat_Mb_start_2016, ProbeSet.BlatSeq, ProbeSet.TargetSeq, IFNULL(ProbeSet.HomoloGeneID, '') AS HomoloGeneID, IFNULL(ProbeSet.UniProtID, '') AS UniProtID, IFNULL(ProbeSet.PubChem_ID, '') AS PubChem_ID, IFNULL(ProbeSet.KEGG_ID, '') AS KEGG_ID, IFNULL(ProbeSet.OMIM, '') AS OMIM, IFNULL(ProbeSet.ChEBI_ID, '') AS ChEBI_ID FROM ProbeSet LEFT JOIN GeneChip ON GeneChip.Id = ProbeSet.ChipId +``` + +The above query results to triples that have the form: + +```text +gn:probeset_probesetidname -> rdf:type -> gnc:probeset +gn:probeset_probesetidname -> rdfs:label -> ProbeSet(Name) +gn:probeset_probesetidname -> skos:altLabel -> ProbeSet(alias) +gn:probeset_probesetidname -> gnt:hasChip -> gn:platform_genechipname +gn:probeset_probesetidname -> gnt:hasTargetId -> TargetId +gn:probeset_probesetidname -> gnt:symbol -> ProbeSet(Symbol) +gn:probeset_probesetidname -> dct:description -> ProbeSetdescription +gn:probeset_probesetidname -> gnt:targetsRegion -> Probe_set_target_region +gn:probeset_probesetidname -> gnt:chr -> ProbeSet(Chr) +gn:probeset_probesetidname -> gnt:mb -> "Mb"^^xsd:double +gn:probeset_probesetidname -> gnt:mbMm8 -> "Mb_mm8"^^xsd:double +gn:probeset_probesetidname -> gnt:mb2016 -> "Mb_2016"^^xsd:double +gn:probeset_probesetidname -> gnt:hasSpecificity -> Probe_set_specificity +gn:probeset_probesetidname -> gnt:hasBlatScore -> Probe_set_BLAT_score +gn:probeset_probesetidname -> gnt:hasBlatMbStart -> "Probe_set_Blat_Mb_start"^^xsd:double +gn:probeset_probesetidname -> gnt:hasBlatMbStart2016 -> "Probe_set_Blat_Mb_start_2016"^^xsd:double +gn:probeset_probesetidname -> gnt:hasBlatMbEnd -> "Probe_set_Blat_Mb_end"^^xsd:double +gn:probeset_probesetidname -> gnt:hasBlatMbEnd2016 -> "Probe_set_Blat_Mb_start_2016"^^xsd:double +gn:probeset_probesetidname -> gnt:hasBlatSeq -> ProbeSetBlatSeq +gn:probeset_probesetidname -> gnt:hasTargetSeq -> ProbeSetTargetSeq +gn:probeset_probesetidname -> gnt:hasHomologeneId -> homologene:HomoloGeneID +gn:probeset_probesetidname -> gnt:hasUniprotId -> uniprot:UniProtID +gn:probeset_probesetidname -> gnt:hasPubChemId -> pubchem:PubChem_ID +gn:probeset_probesetidname -> gnt:hasKeggId -> kegg:KEGG_ID +gn:probeset_probesetidname -> gnt:hasOmimId -> +gn:probeset_probesetidname -> gnt:hasChebiId -> chebi:ChEBI_ID +``` +Here's an example query: + +```sparql +PREFIX gn: <http://genenetwork.org/id/> +PREFIX probeset: <http://genenetwork.org/probeset/> +PREFIX gnc: <http://genenetwork.org/category/> +PREFIX gnt: <http://genenetwork.org/term/> +PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> +PREFIX kegg: <http://bio2rdf.org/ns/kegg#> +PREFIX pubchem: <https://pubchem.ncbi.nlm.nih.gov/> +PREFIX omim: <https://www.omim.org/entry/> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX uniprot: <http://purl.uniprot.org/uniprot/> +PREFIX chebi: <http://purl.obolibrary.org/obo/CHEBI_> +PREFIX dct: <http://purl.org/dc/terms/> +PREFIX owl: <http://www.w3.org/2002/07/owl#> +PREFIX homologene: <https://bio2rdf.org/homologene:> +PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> +PREFIX skos: <http://www.w3.org/2004/02/skos/core#> + +SELECT * WHERE { + ?s rdf:type gnc:probeset . + ?s rdfs:label "100001_at" . + ?s skos:altLabel "T3g; Ctg3; Ctg-3" . + ?s gnt:hasChip gn:platform_mg_u74av2 . + ?s ?p ?o . +} +``` + +Expected Result: + +```rdf +gn:probeset_100001_at rdf:type gnc:probeset . +gn:probeset_100001_at rdfs:label "100001_at" . +gn:probeset_100001_at skos:altLabel "T3g; Ctg3; Ctg-3" . +gn:probeset_100001_at gnt:hasChip gn:platform_mg_u74av2 . +gn:probeset_100001_at gnt:symbol "Cd3g" . +gn:probeset_100001_at dct:description "CD3d antigen, gamma polypeptide" . +gn:probeset_100001_at gnt:chr "9" . +gn:probeset_100001_at gnt:mb "44.970689"^^xsd:double . +gn:probeset_100001_at gnt:mbMm8 "44.721684"^^xsd:double . +gn:probeset_100001_at gnt:mb2016 "44.778772"^^xsd:double . +gn:probeset_100001_at gnt:hasSpecificity "9.3" . +gn:probeset_100001_at gnt:hasBlatScore "186" . +gn:probeset_100001_at gnt:hasBlatMbStart "44.970689"^^xsd:double . +gn:probeset_100001_at gnt:hasBlatMbStart2016 "44.778772"^^xsd:double . +gn:probeset_100001_at gnt:hasBlatMbEnd "44.971291"^^xsd:double . +gn:probeset_100001_at gnt:hasBlatMbEnd2016 "44.778772"^^xsd:double . +gn:probeset_100001_at gnt:hasBlatSeq "CTCTGTTGCAAAATGAACAGCTGTACAGCCCCTCAAGGACCGGGAATATGACCAGTACAGCCATCTCCAAGGAAACCAACTGAGGAAGAAGTGAACTCAGCAGGACTCAGGGTGTCCCCACAATGCATTTTGGAGAGAGCCCAGACTGCAAGCAGAGAGGAAGAACTGAGGAAAACAAGCACAGCGTGGTGTT" . +gn:probeset_100001_at gnt:hasTargetSeq "ctctgttgcaaaatgaacagctgtaccagcccctcaaggaccgggaatatgaccagtacagccatctccaaggaaaccaactgaggaagaagtgaactcagcaggactcagggtgtccccccttntatccagcacccagaatcaaaacaatgcattttggagagagcccagtagagagattttcaaccctacaggtagactgcaagcagagaggaagaactgtcaaagaaattttggtcttttttttttttttnncaaaataaaataaaagcttggaggagccagtggtatgantnnnnnntgnancanttgtcaaccttgtttggggttnncagcaccccacccccagaccccccaaaaaaattcagtgaaggaaaacaagcacagcgtggtgtt" . +gn:probeset_100001_at gnt:hasHomologeneId homologene:55 . +gn:probeset_100001_at gnt:hasOmimId omim:186740 . +``` + |